Compositions and methods comprising bacteria for improving behavior in neurodevelopmental disorders

ABSTRACT

Some embodiments include bacterial species for use in treatment of one or more autism spectrum disorder (ASD), and/or schizophrenia symptoms in a subject in need thereof. The subject in need thereof can have a gut microbiota signature characteristic of an adult. The bacterial species can include  Bacteroides  (e.g.,  B. fragilis, B. thetaiotaomicron , and/or  B. vulgatus ), and/or  Enterococcus  (e.g.,  E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum , or  E. casseliflavus ). Upon treatment, one or more ASD-related behaviors can be improved in the subject.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent application Ser. No. 16/140,013, filed on Sep. 24, 2018, which is a continuation of U.S. patent application Ser. No. 14/925,510, filed Oct. 28, 2015, which issued as U.S. Pat. No. 10,111,914, on Oct. 30, 2018, and which claims the benefit of U.S. Provisional Application No. 62/072,905, filed Oct. 30, 2014, each of which is hereby incorporated by reference in its entirety.

STATEMENT REGARDING FEDERALLY SPONSORED R&D

This invention was made with government support under Grant No. MH100556 awarded by the National Institutes of Health. The government has certain rights in the invention.

BACKGROUND Background

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is diagnosed based on presentation with repetitive behaviors and impaired social interaction and communication. The prevalence of ASD in the United States is currently a striking 1 in 68, representing a significant medical and social issue. Although the underlying causes of ASD are largely unknown, both genetic and environmental risk factors are implicated.

Field

Some embodiments described herein relate generally to probiotic compositions, which can be used to treat autism spectrum disorder (ASD) symptoms. In some embodiments, the probiotic compositions can be used to treat ASD symptoms in an individual having an adult microbiotic profile.

SUMMARY

In accordance with some embodiments descried herein, a method for improving behavioral performance in a human. The method can comprise identifying a human subject having a gut microbiota signature comprising at least 500 different species of microbes. The method can comprise administering to the human subject an effective amount of one or more Bacteroides bacteria. In some embodiments, the method further comprises identifying the gut microbiota signature of the human subject as an adult gut microbiotia signature. In some embodiments, the subject suffers from anxiety, autism spectrum disorder (ASD), schizophrenia, or a pathological condition with one or more of the symptoms of ASD or schizophrenia. In some embodiments, the method further comprises the effective amount of one or more Bacteroides bacteria comprises B. fragilis. In some embodiments the effective amount of one or more Bacteroides bacteria comprises B. fragilis, B. thetaiotaomicron, B. vulgatus, or a mixture of two or three of the listed bacteria, for example B. fragilis and B. thetaiotaomicron, B. fragilis and B. vulgatus, B. thetaiotaomicron and B. vulgatus, or B. fragilis, B. thetaiotaomicron, and B. vulgatus. In some embodiments, the method further comprises administering an amount of Enterococcus bacteria to the subject. In some embodiments, a sole active ingredient administered to the subject in the method consists essentially of one or more Bacteroides bacteria. In some embodiments, a sole active ingredient administered to the subject consists essentially of B. fragilis. In some embodiments, the effective amount of one or more Bacteroides bacteria is in a composition substantially free of bacteria other than the Bacteroides bacteria. In some embodiments, the effective amount of Bacteroides bacteria is in a composition substantially free of bacteria other than B. fragilis. In some embodiments, the effective amount of one or more Bacteroides bacteria is administered orally. In some embodiments, improving behavioral performance comprises improving a communication behavior, a repetitive behavior, anxiety, or a combination of two or three of these listed behaviors. In some embodiments, the human subject is an adult.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A and FIG. 1B are a series of graphs that treatment of adult maternal immune activation (MIA) mice with a probiotic comprising B. fragilis corrects deficits in exploratory behavior in accordance with some embodiments described herein. FIG. 1A depicts entries into the center area. FIG. 1B depicts total distance traveled.

FIG. 2 is a graph demonstrating that treatment of adult MIA mice with a probiotic comprising B. fragilis reduces repetitive behavior in accordance with some embodiments described herein.

FIG. 3 is a graph demonstrating that treatment of adult MIA mice with a probiotic comprising B. fragilis increases communication behavior in accordance with some embodiments described herein.

DETAILED DESCRIPTION

In the following detailed description, reference is made to the accompanying drawings, which form a part hereof. In the drawings, similar symbols typically identify similar components, unless context dictates otherwise. The illustrative embodiments described in the detailed description, drawings, and claims are not meant to be limiting. Other embodiments may be utilized, and other changes may be made, without departing from the spirit or scope of the subject matter presented herein. It will be readily understood that the aspects of the present disclosure, as generally described herein, and illustrated in the Figures, can be arranged, substituted, combined, separated, and designed in a wide variety of different configurations, all of which are explicitly contemplated herein.

Without being limited by any theory, it is contemplated that there can be a gut-immune-brain connection in autism spectrum disorders (ASD). As gut microbiomes can differ in infants and “adults” (three years old or greater), it is contemplated that probiotics do not necessarily have the same effect on an infant gut microbiome as an adult gut microbiome, and thus are not necessarily interchangeable between infants and adults. In accordance with some embodiments described herein, probiotics comprising one or more bacterial species are provided, which can be administered to a subject to treat one or more symptoms of ASD and/or or schizophrenia, and having a gut microbiota signature characteristic of an adult. The ASD and/or schizophrenia symptoms, for example repetitive behavior, anxiety, and deficient communication behavior can be improved following administration of the probiotic, as described herein. In some embodiments, the probiotic comprises one or more of the following bacteria: Bacteroides fragilis, Bacteroides thetaiotaomicron, Bacteroides vulgatus, and Enterococcus faecalis. The probiotic can improve repetitive behavior, anxiety, and communication behavior in the subject having an adult gut microbiome.

Maternal infection is identified as a primary non-genetic cause of ASD, based on many large epidemiological studies linking maternal bacterial or viral infection during pregnancy increased risk for ASD in the offspring, and on pre-clinical studies in mice, rats and monkeys demonstrating that maternal infection or immune activation during pregnancy yields offspring with behavioral and neuropathological abnormalities relevant to ASD. ASD is also co-morbid with a variety of medical conditions, ranging from seizures to immune dysregulation. Gastrointestinal issues, such as constipation, abdominal pain, intestinal permeability and altered composition of the gut microbiota are prevalent in a significant subset of ASD individuals. Collectively, increasing evidence implicates a potential role for gut-brain interactions in the etiopathogenesis of ASD.

It is noted that, in addition to displaying cardinal behavioral and neuropathological features of ASD and schizophrenia, the maternal immune activation (MIA) mouse model for autism also exhibits ASD-related immunological and gastrointestinal abnormalities. Further, treating MIA offspring at weaning with the human commensal bacterium, Bacteroides fragilis, corrects gastrointestinal and behavioral deficits. The gut microbiota is inherited during the birthing process, after which it develops and matures until it reaches an adult microbiota signature based on species composition and abundance. It is contemplated that in accordance with some embodiments described herein, B. fragilis provides a potential probiotic treatment for symptoms of ASD and/or schizophrenia.

To examine the ability of B. fragilis to correct ASD and schizophrenia behavioral abnormalities during adulthood, adult MIA mouse offspring were treated with B. fragilis at 6 weeks of age and then effects on ASD-related behavioral performance were examined. It was observed that treatment of ASD and schizophrenia model offspring with B. fragilis (in comparison to untreated controls), corrected anxiety and deficiencies in exploratory behaviors associated with ASD and schizophrenia (see FIG. 1). It was observed that treatment of ASD and schizophrenia model offspring with B. fragilis (in comparison to untreated controls) corrected deficiencies in repetitive behaviors associated with ASD and schizophrenia (see FIG. 2). It was also observed that treatment of ASD and schizophrenia model offspring with B. fragilis (in comparison to untreated controls), corrected deficiencies in communication behaviors associated with ASD and schizophrenia (see FIG. 3). As such, it is contemplated that in accordance with some embodiments described herein, treatment of a subject having ASD or schizophrenia and having an adult gut microbiota signature can ameliorate the symptoms of ASD and/or schizophrenia. By way of the example, the symptoms can include at least one of: anxiety, repetitive behavior, and deficient communication behavior.

Definitions

Unless defined otherwise, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the present disclosure belongs. See, e.g. Singleton et al., Dictionary of Microbiology and Molecular Biology 2nd ed., J. Wiley & Sons (New York, N.Y. 1994); Sambrook et al., Molecular Cloning, A Laboratory Manual, Cold Springs Harbor Press (Cold Springs Harbor, N.Y. 1989). For purposes of the present disclosure, the following terms are defined below.

As used herein, the term “subject” is a vertebrate, such as a mammal. The term “mammal” is defined as an individual belonging to the class Mammalia and includes, without limitation, humans, domestic and farm animals, and zoo, sports, or pet animals, such as sheep, dogs, horses, cats or cows. In some embodiments, the subject is human. In some embodiments, the subject is a non-human primate.

As used herein, the term “condition/disorder/symptom” or “behavioral abnormality” refers to a symptom expressed by a subject including but not limited to anxiety, Fragile X, Rett syndrome, tuberous sclerosis, obsessive compulsive disorder, attention deficit disorder, schizophrenia, autistic disorder (classic autism), Asperger's disorder (Asperger syndrome), pervasive developmental disorder not otherwise specified (PDD-NOS), childhood disintegrative disorder (CDD), or a pathological condition with one or more of the symptoms of ASD.

As used herein, the term “subject in need of the treatment” refers to a subject expressing or suffering from one or more of the behavioral disorder/symptoms mentioned above. In some embodiments, the subject in need of treatment suffers from at least one of schizophrenia, ASD, or a gastrointestinal or immunological pathology associated with ASD or schizophrenia (for example leaky gut syndrome). An appropriately qualified person is able to identify such an individual in need of treatment using standard behavioral testing protocols/guidelines. The same behavioral testing protocols/guidelines can also be used to determine whether there is improvement to the individual's disorder and/or symptoms.

As used herein, the term “improvement in behavioral performance” refers to prevention or reduction in the severity or frequency, to whatever extent, of one or more of the behavioral disorders, symptoms and/or abnormalities expressed by individual suffering from ASD, schizophrenia, or a pathological condition with one or more of the symptoms of ASD or schizophrenia. Non-limiting examples of the behavioral symptoms include impaired communication, impaired sociability, impaired language comprehension and/or production, repetitive behavior, and increased anxiety. The improvement is either observed by the individual taking the treatment themselves or by another person (medical or otherwise). In some embodiments, a probiotic comprising an effective amount of Bacteroides and/or Enterococcus bacteria as described herein is administered the subject. In some embodiments, sensorimotor gating behavior is improved in the subject after administration of the probiotic. In some embodiments, communication behavior is improved in the subject after administration of the probiotic. As used herein, “communication behavior” refers to communication, language comprehension and production, and sociability, including vocal and non-vocal social communication. In some embodiments, a subject is identified as deficient in communication behavior based on impaired sociability. In some embodiments, a subject is identified as deficient in communication behavior based on impaired language comprehension and/or production.

As used herein, the term “treatment” refers to a clinical intervention made in response to a disease, disorder or physiological condition manifested by a subject, particularly a subject suffering from ASD, schizophrenia, or a pathological condition with one or more of the symptoms of ASD or schizophrenia. The aim of treatment may include, but is not limited to, one or more of the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and the remission of the disease, disorder or condition. In some embodiments, “treatment” refers to both therapeutic treatment and prophylactic or preventative measures. Those in need of treatment include those already affected by a disease or disorder or undesired physiological condition as well as those in which the disease or disorder or undesired physiological condition is to be prevented. For example, in some embodiments treatment may improve behavioral performance of the subject, including ASD-related behaviors such as sensorimotor gating behavior deficiencies and/or communication behavior deficiencies. As used herein, the term “prevention” refers to any activity that reduces the burden of the individual later expressing those behavioral symptoms. This takes place at primary, secondary and tertiary prevention levels, wherein: a) primary prevention avoids the development of symptoms/disorder/condition; b) secondary prevention activities are aimed at early stages of the condition/disorder/symptom treatment, thereby increasing opportunities for interventions to prevent progression of the condition/disorder/symptom and emergence of symptoms; and c) tertiary prevention reduces the negative impact of an already established condition/disorder/symptom by, for example, restoring function and/or reducing any condition/disorder/symptom or related complications.

“Pharmaceutically acceptable” carriers are ones which are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. “Pharmaceutically acceptable” carriers in accordance with methods and uses and compositions and kits herein can comprise, but not limited to, organic or inorganic, solid or liquid excipients which is suitable for the selected mode of application such as oral application or injection, and administered in the form of a conventional pharmaceutical preparation, such as solid such as tablets, granules, powders, capsules, and liquid such as solution, emulsion, suspension and the like. Often the physiologically acceptable carrier is an aqueous pH buffered solution such as phosphate buffer or citrate buffer. The physiologically acceptable carrier may also comprise one or more of the following: antioxidants including ascorbic acid, low molecular weight (less than about 10 residues) polypeptides, proteins, such as serum albumin, gelatin, immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone, amino acids, carbohydrates including glucose, mannose, or dextrins, chelating agents such as EDTA, sugar alcohols such as mannitol or sorbitol, salt-forming counterions such as sodium, and nonionic surfactants such as and nonionic surfactants such as TWEEN™ surfactant, polyethylene glycol (PEG), and PLURONICS™ surfactant. Auxiliary, stabilizer, emulsifier, lubricant, binder, pH adjustor controller, isotonic agent and other conventional additives may also be added to the carriers.

The pharmaceutically acceptable or appropriate carrier in accordance with methods and uses and compositions and kits herein may include other compounds known to be beneficial to an impaired situation of the GI tract, (e.g., antioxidants, such as Vitamin C, Vitamin E, Selenium or Zinc); or a food composition. The food composition can be, but is not limited to, milk, yoghurt, curd, cheese, fermented milks, milk based fermented products, ice-creams, fermented cereal based products, milk based powders, infant formulae, tablets, liquid bacterial suspensions, dried oral supplement, or wet oral supplement.

As used herein, the term “probiotic” refers to live microorganisms, which, when administered in adequate amounts, confer a health benefit on the host. The probiotics in accordance with methods and uses and compositions and kits herein may be available in foods and dietary supplements (for example, but not limited to capsules, tablets, powders, and liquids). Non-limiting examples of foods containing probiotic include dairy products such as yogurt, fermented and unfermented milk, smoothies, butter, cream, hummus, kombucha, salad dressing, miso, tempeh, nutrition bars, and some juices and soy beverages. In some embodiments, the probiotic comprises a single microorganism. In some embodiments, the probiotic comprises a combination of microorganisms. In some embodiments, the probiotic comprises a single composition. In some embodiments, the probiotic comprises two or more compositions, which can be used together, for example administered simultaneously or administered sequentially. It is noted that a probiotic can serve as the “active ingredient” or a composition or compositions for use in administration to a subject. That is, the method, use, and/or composition or compositions (either individually or in the aggregate) can comprise an effective amount of probiotic to improve at least one behavior in a subject. In some embodiments, the probiotic is the sole active ingredient for administration to the subject. In some embodiments, the “sole active ingredient” probiotic for administration to the subject can be provided in a composition or in a method or use that is substantially free of or free of bacteria other than the probiotic, antibiotics, and drugs. Even if the probiotic is the “sole” active ingredient, the composition or composition comprising the probiotic may comprise additional substances (such as buffers, bacterial feedstock, excipients, flavors, and/or food) that do not substantially affect the behavior of the subject, but may be useful for the function of the probiotic or its administration.

In some embodiments, the probiotic is comprised in a composition or compositions that are substantially free of bacteria (other than the probiotic) and/or drugs or antibiotics. By “substantially free” or “substantially absent”, it is understood that while a bacteria other than the probiotic, drug, and/or antibiotic may be present in trace amounts, the bacteria other than the probiotic, drug, and/or antibiotic have no appreciable effect on the subject.

As used herein “effective amount” of probiotic refers to a quantity sufficient to achieve a clinically significant change in a behavior of a subject.

As used herein, the term “nutraceutical” refers to a food stuff (as a fortified food or a dietary supplement) that provides health benefits. Nutraceutical foods are not subject to the same testing and regulations as pharmaceutical drugs.

The term “microbiota signature” (or optionally “gut microbiota signature”), including pluralizations and variations of this root term, as used herein refers to a profile of a microbiota in a gut, and can include overall number of microbial organisms in the gut, and/or relative abundance of particular phyla and/or species of microbiota in the gut. An “adult microbiota signature” (or optionally “adult gut microbiota signature”), including pluralizations and variations of this root term, as used herein refers to a microbiota signature characteristic of a human who is at least three years of age. The term “infant microbiota signature” (or optionally “infant gut microbiota signature”), including pluralizations and variations of this root term, as used herein refers to a microbiota signature characteristic of a human under three years of age. As used herein, the term “adult” refers to a human who is at least three years of age.

Without being limited by any theory, a microbiota signature can be affected by environmental factors and life events, for example diet, hygiene, infection or other illness, and developmental events for example hormonal shifts. An infant (under three years old) that is at weaning or immediately post-weaning can be expected to have different microbiome characteristics (and thus a different microbiota signature) than an older individual that has been eating a greater variety of foods, had greater exposure to infection and the like. Accordingly, without being limited by any theory, interventions that affect an individual with an infant microbiota signature (for example probiotic treatments) are not necessarily expected to have comparable or analogous in individuals with an adult microbiota signature, because the infant gut microbiome can differ substantially from the adult microbiome.

A typical newborn gut can have about 100 different species of microbes, while a typical adult (age three years or greater) gut can have about 1000 different species of microbes. In some embodiments an adult gut microbiota signature is characterized by at least about 500 different species of microbes, for example at least about 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, or 1500 different species, including ranges between any two of the listed values. In some embodiments, an infant gut microbiome has a lower number of total species of microbes than an adult gut microbiome. Optionally, a microbiota signature can also be characterized by relative abundance of various phyla (this metric can be used alone, or in conjunction with total number of different species). In some embodiments, an infant (i.e. under three years of age) gut microbiota signature is characterized by a relative abundance of the following phyla (in order of greatest to least) of Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes. In some embodiments, an adult gut microbiota signature is characterized by a relative abundance of the following phyla (in order of greatest to least) of: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria. In some embodiments, an elderly adult gut microbiota signature is characterized by a relative abundance of the following phyla: Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria. As such, in some embodiments, an adult gut microbiota signature is characterized by a relative abundance of the following phyla (in order of greatest to least) of: (a) Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, or (b) Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria.

In some embodiments, a gut microbiota signature can be characterized by analysis of the composition of a sample from a subject representative of the gut, for example a fecal sample, or an intestinal biopsy or brush sample. The number of different species in a gut sample and/or the relative makeup of species and/or phyla in a gut sample can be ascertained by identifying nucleic acids characteristic of the different phyla. For example, the sequences of relatively conserved nucleic acids such as the 16s rRNA subunit can be compared. The comparison can be performed by a number of techniques known to one skilled in the art, for example, nucleic acid analysis such microarray analysis, nucleic acid sequencing (such as multiplex sequencing), polymerase chain reaction (such as conventional polymerase chain reaction, and/or quantitative polymerase chain reaction), hybridization of nucleic acid probes, and the like. The nucleic acids can be aligned to references to ascertain the microbial species present in the sample.

Probiotics for Treatment of ASD and/or Schizophrenia

Without being limited by any theory, it is contemplated that the MIA mouse model for autism, which displays both neuropathological and behavioral features of ASD and also schizophrenia, and also exhibits immunological and gastrointestinal abnormalities, is relevant to the corresponding human disorder. It is demonstrated herein that treatment of MIA offspring with human commensal bacteria such as Bacteroides fragilis corrects particular gastrointestinal and behavioral deficits in subjects having adult gut microbiota gut signatures. Accordingly, some embodiments include a probiotic treatment and/or prevention for symptoms of ASD and/or schizophrenia in subjects having an adult gut microbiota gut signature.

In some embodiments, the subject is in need of improvement of anxiety, repetitive behavior, and communication behavior (for example, communication, language comprehension and production, and sociability, including vocal and non-vocal social communication). An effective amount of a probiotic comprising, consisting of, or consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the anxiety, repetitive behavior, and deficient communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbial phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in anxiety, repetitive behavior, and deficient communication behavior has ASD. In some embodiments, the subject in need of improvement in anxiety, repetitive behavior, and communication behavior has schizophrenia. In some embodiments, the communication behavior to be improved comprises at least one of: communication, language comprehension and production, and sociability. In some embodiments, the subject in need of improvement in anxiety, repetitive behavior, and communication behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in communication behavior (e.g. language comprehension and/or production, sociability, and/or communication). An effective amount of a probiotic comprising, consisting of, or consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in communication behavior has ASD. In some embodiments, the subject in need of improvement in communication behavior has schizophrenia. In some embodiments, the communication behavior to be improved comprises at least one of: communication, language comprehension and production, and sociability. In some embodiments, the subject in need of improvement in communication behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in repetitive behavior. An effective amount of a probiotic comprising, consisting of, or consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. In some embodiments, the adult gut microbiotic signature is identified as comprising a relative abundance of microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in repetitive behavior has ASD. In some embodiments, the subject in need of improvement in repetitive behavior has schizophrenia. In some embodiments, the subject in need of improvement in repetitive behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in anxiety. An effective amount of a probiotic comprising, consisting of or, consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in anxiety has ASD. In some embodiments, the subject in need of improvement in anxiety has schizophrenia. In some embodiments, the subject in need of improvement in anxiety is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in repetitive behavior and communication behavior (including language comprehension and/or production, sociability, and communication). An effective amount of a probiotic comprising, consisting of or, or consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in repetitive behavior and communication behavior has ASD. In some embodiments, the subject in need of improvement in repetitive behavior and communication behavior has schizophrenia. In some embodiments, the communication behavior to be improved comprises at least one of: communication, language comprehension and production, and sociability. In some embodiments, the subject in need of improvement in repetitive behavior and communication behavior has ASD. In some embodiments, the subject in need of improvement in repetitive behavior and communication behavior has schizophrenia. In some embodiments, the subject in need of improvement in repetitive behavior and communication behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in anxiety and communication behavior (including language comprehension and/or production, sociability, and communication). An effective amount of a probiotic comprising, consisting of or, consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. In some embodiments, the adult gut microbiotic signature is identified as comprising a relative abundance of microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in anxiety and communication behavior has ASD. In some embodiments, the subject in need of improvement in anxiety and communication behavior has schizophrenia. In some embodiments, the communication behavior to be improved comprises at least one of: communication, language comprehension and production, and sociability. In some embodiments, the subject in need of improvement in anxiety and communication behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the subject is in need of improvement in anxiety and repetitive behavior. An effective amount of a probiotic comprising, consisting of or, consisting essentially of at least one of the following is provided for administration to the subject (or is for use in treating the subject): (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Following administration of the bacteria, the communication behavior can be improved. Optionally, the subject is identified as having a gut microbiotic signature comprising at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. Optionally, the B. fragilis comprises wild-type B. fragilis, mutant B. fragilis lacking polysaccharide A (dPSA), or a combination of wild-type B. fragilis and dPSA B. fragilis. In some embodiments, the subject in need of improvement in anxiety and repetetive behavior has ASD. In some embodiments, the subject in need of improvement in anxiety and repetitive behavior has schizophrenia. In some embodiments, the subject in need of improvement in anxiety and repetitive behavior is at least three years old, for example at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 years old, including ranges between any two of the listed values.

In some embodiments, the probiotic comprises any of the above-disclosed bacterial species or combinations of bacterial species, and is provided for administration to the subject (or is for administration to the subject) in a single probiotic composition. In some embodiments, the probiotic comprises any of the above-referenced bacterial species or combinations of bacterial species, and is administered to the subject (or is for administration to the subject) in two or more different probiotic compositions. For example, a probiotic of “bacteria A and bacteria B” can be administered either in a single composition comprising bacteria A and bacteria B, or in a first composition comprising bacteria A in conjunction with a second composition comprising bacteria B. In some embodiments, first and second compositions are administered simultaneously. In some embodiments, the first and second compositions are administered separately.

In some embodiments, a probiotic comprising a combination of Bacteroides bacteria as described herein is provided as a first composition comprising a first Bacteroides bacterium or combination of Bacteroides bacteria, and a second composition comprising a second Bacteroides bacterium or combination of Bacteroides bacteria as described herein. In some embodiments, a probiotic comprising a combination of Enterococcus bacteria and Bacteroides bacteria as described herein is provided as a first composition comprising the Enterococcus bacteria, and a second composition comprising the Bacteroides bacteria or combination of Bacteroides bacteria as described herein. In some embodiments, the Enterococcus bacteria and a first Bacteroides bacteria (or combination of Bacteroides bacteria) are administered in a first composition, and the Enterococcus bacteria and a second Bacteroides bacteria (or combination of Bacteroides bacteria) that is different from the first are administered in a second composition. In some embodiments, the Enterococcus bacteria and a first Bacteroides bacteria (or combination of Bacteroides bacteria) are administered in a first composition, and a second Bacteroides bacteria (or combination of Bacteroides bacteria) that is different from the first is administered in a second composition.

In accordance with any of the embodiments described above, optionally, each composition, use, or method is free of, or is substantially free of bacteria other than the identified bacteria of the probiotic. In accordance with any of the embodiments described above, optionally, each composition is free of, or is substantially free of antibiotics. In accordance with any of the embodiments described above, optionally, each composition is free of, or is substantially free of bacteria other than the probiotic and antibiotics.

In accordance with embodiments described herein, the probiotics of the methods, uses, and compositions described herein can be for any suitable route of administration. For example, the probiotic can be administered to the subject via oral administration, rectum administration, transdermal administration, intranasal administration or inhalation. In some embodiments, the probiotic is administered to the subject orally.

In some embodiments, the effective amount of bacteria in the probiotic composition, use, or method includes at least about 10⁴ colony forming units (cfu), for example at least about 10⁴, 10⁵, 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹², or 10¹³ cfu, including ranges between any of the listed values, for example 10⁴-10⁸ cfu, 10⁴-10⁹ cfu, 10⁴-10¹⁰ cfu, 10⁴-10¹¹ cfu, 10⁴-10¹² cfu, 10⁴-10¹² cfu, 10⁵-10⁸ cfu, 10⁵-10⁹ cfu, 10⁵-10¹⁰ cfu, 10⁵-10¹¹ cfu, 10⁵-10¹² cfu, 10⁵-10¹² cfu, 10⁶-10⁸ cfu, 10⁶-10⁹ cfu, 10⁶-10¹⁰ cfu, 10⁶-10¹¹ cfu, 10⁶-10¹² cfu, 10⁶-10¹² cfu, 10⁷-10⁸ cfu, 10⁷-10⁹ cfu, 10⁷-10¹⁰ cfu, 10⁷-10¹¹ cfu, 10⁷-10¹² cfu, 10⁷-10¹² cfu, -10⁹ cfu, 10⁸-10¹⁰ cfu, 10⁸-10¹¹ cfu, 10⁸-10¹² cfu, or 10⁸-10¹² cfu. In some embodiments, the effective amount of bacteria comprises a log phase quantity (at 37° C.) of bacteria in a composition for administration to the subject. In some embodiments, the effective amount of bacteria comprises a stationary phase quantity (at 37° C.) of bacteria in a composition for administration to the subject.

Methods of Treating and/or Preventing Symptoms of ASD and/or Schizophrenia

In some embodiments, methods of treating ASD and/or schizophrenia symptoms are provided. The method can comprise identifying the subject can as in need of improving an anxiety, repetitive behavior, and/or communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprising administering an effective amount of a probiotic comprising, consisting essentially or, consisting of Enterococcus bacteria, Bacteroides bacteria, or a combination of Enterococcus bacteria and Bacteroides bacteria as described herein is administered to the subject in need of behavioral improvement. The subject can exhibit improved anxiety, repetitive behavior, or communication behavior following administration of the probiotic. In some embodiments, the subject is in need of improved anxiety, and following administration of the probiotic, anxiety is improved. In some embodiments, the subject is in need of improved communication behavior, and following administration of the probiotic, communication behavior is improved. In some embodiments, the subject is in need of improved anxiety and repetitive behavior, and following administration of the probiotic, communication behavior is improved. In some embodiments, the subject is in need of improved anxiety and communication behavior, and following administration of the probiotic, communication behavior is improved. In some embodiments, the subject is in need of improved repetitive behavior and communication behavior, and following administration of the probiotic, communication behavior is improved. In some embodiments, the communication behavior in need of improvement (and that is improved after administration of the probiotic) comprises at least one of communication, sociability, or language comprehension and/or language production. In some embodiments, the subject is further identified as in need of improvement of defects in intestinal barrier integrity, and following administration of the probiotic, the defects in defects in intestinal barrier integrity are improved. Optionally the subject is at least three years old.

In some embodiments, methods of treating ASD symptoms are provided. The method can comprise identifying a subject as in need of improving anxiety, repetitive behavior, and/or communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprise administering a probiotic comprising, consisting essentially of, or consisting of an effective amount of Bacteroides bacteria, or a combination of Bacteroides and Enterococcus bacteria as described herein. The anxiety, repetitive behavior, and/or communication behavior can be improved following administration of the probiotic. In some embodiments, the method comprises determining the subject to be in need of improving anxiety and repetitive behavior. Following administration of the probiotic, anxiety and repetitive behavior can be improved. Optionally the subject is at least three years old. In some embodiments, the method comprises determining the subject to be in need of improving anxiety and communication behavior. Following administration of the probiotic, anxiety and communication behavior can be improved. In some embodiments, the method comprises determining the subject to be in need of improving repetitive behavior and communication behavior. Following administration of probiotic, the repetitive behavior and communication behavior are improved. In some embodiments, the method comprises determining the subject to be in need of improving anxiety, communication behavior, and repetitive behavior, and following administration of the probiotic, anxiety, communication behavior, and repetitive behavior are improved. In some embodiments, the communication behavior in need of improvement (and subsequently improved) comprises at least one of communication, sociability, or language comprehension and/or language production. In some embodiments, the method further comprises determining whether or not the subject has ASD. In some embodiments, the ASD symptoms are treated. In some embodiments, the subject is further identified as in need of improvement of defects in intestinal barrier integrity, and following administration of the probiotic, the defects in defects in intestinal barrier integrity are improved.

In some embodiments, methods of treating schizophrenia symptoms are provided. The method can comprise identifying a subject as in need of improving anxiety, repetitive behavior, and/or communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprise administering a probiotic comprising, consisting essentially of, or consisting of an effective amount of Bacteroides bacteria, or a combination of Bacteroides and Enterococcus bacteria as described herein. The anxiety, repetitive behavior, and/or communication behavior can be improved following administration of the probiotic. In some embodiments, the method comprises determining the subject to be in need of improving anxiety and repetitive behavior. Following administration of the probiotic, anxiety and repetitive behavior can be improved. Optionally the subject is at least three years old. In some embodiments, the method comprises determining the subject to be in need of improving anxiety and communication behavior. Following administration of the probiotic, anxiety and communication behavior can be improved. In some embodiments, the method comprises determining the subject to be in need of improving repetitive behavior and communication behavior. Following administration of probiotic, the repetitive behavior and communication behavior are improved. In some embodiments, the method comprises determining the subject to be in need of improving anxiety, communication behavior, and repetitive behavior, and following administration of the probiotic, anxiety, communication behavior, and repetitive behavior are improved. In some embodiments, the communication behavior in need of improvement (and subsequently improved) comprises at least one of communication, sociability, or language comprehension and/or language production. In some embodiments, the method further comprises determining whether or not the subject has schizophrenia. In some embodiments, the schizophrenia symptoms are treated. In some embodiments, the subject is further identified as in need of improvement of defects in intestinal barrier integrity, and following administration of the probiotic, the defects in defects in intestinal barrier integrity are improved.

In some embodiments, methods of preventing ASD and/or schizophrenia symptoms are provided. The method can comprise identifying a subject as at risk of developing anxiety, repetitive behavior, and/or deficient communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprise administering a probiotic comprising, consisting essentially of, or consisting of an effective amount of Bacteroides bacteria, or a combination of Bacteroides and Enterococcus bacteria as described herein. The subject can develop with minimized deficiencies or no discernable deficiencies in anxiety, repetitive behavior, and/or communication behavior. In some embodiments, the subject is determined to be at risk for developing anxiety. Following administration of the probiotic, the subject can develop with minimal or no anxiety. Optionally, the at-risk subject is a child, adolescent, or adult three years old or older. In some embodiments, the subject is determined to be at risk for developing repetitive behavior. Following administration of the probiotic, the subject can develop with minimal or no repetitive behavior. In some embodiments, the subject is determined to be at risk for developing deficient communication behavior. Following administration of the probiotic, the subject can develop with minimal or no deficiencies in communication behavior. In some embodiments, the communication behavior that develops without discernable deficiencies includes at least one of language comprehension and/or production, sociability, or communication. In some embodiments, the method further comprises determining whether the subject is at risk for ASD. In some embodiments, ASD symptoms are prevented. In some embodiments, the method further comprises determining whether the subject is at risk for schizophrenia. In some embodiments, schizophrenia symptoms are prevented. In some embodiments, ASD and schizophrenia symptoms are prevented.

In some embodiments, methods of preventing ASD symptoms are provided. The method can comprise identifying a subject as at risk of developing anxiety, repetitive behavior, and/or deficient communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprise administering a probiotic comprising, consisting essentially of, or consisting of an effective amount of Bacteroides bacteria, or a combination of Bacteroides and Enterococcus bacteria as described herein. The subject can develop with minimized deficiencies or no discernable deficiencies in anxiety, repetitive behavior, and/or communication behavior. Optionally, the at-risk subject is a child, adolescent, or adult three years old or older. In some embodiments, the subject is determined to be at risk for developing anxiety. Following administration of the probiotic, the subject can develop with minimal or no anxiety. In some embodiments, the subject is determined to be at risk for developing repetitive behavior. Following administration of the probiotic, the subject can develop with minimal or no repetitive behavior. In some embodiments, the subject is determined to be at risk for developing deficient communication behavior. Following administration of the probiotic, the subject can develop with minimal or no deficiencies in communication behavior. In some embodiments, the communication behavior that develops without discernable deficiencies includes at least one of language comprehension and/or production, sociability, or communication. In some embodiments, the method further comprises determining whether the subject is at risk for ASD. In some embodiments, ASD symptoms are prevented.

In some embodiments, methods of preventing schizophrenia symptoms are provided. The method can comprise identifying a subject as at risk of developing anxiety, repetitive behavior, and/or deficient communication behavior. Optionally, the method can comprise determining a gut microbiotic signature of the subject from a sample of the subject. Optionally, the subject is determined to be amenable to the method of treatment if the gut microbiotic signature of the subject comprises at least 500 different species of microbes, for example at least 500, 600, 700, 800, 900, 1000, 111, 1200, 1300, 1400, or 1500 different species, including ranges between any two of the listed values. Optionally the subject is identified as having an adult gut microbiotic signature. Optionally, the adult gut microbiotic signature is identified based on relative quantities of particular microbiotic phyla as described herein. The method can comprise administering a probiotic comprising, consisting essentially of, or consisting of an effective amount of Bacteroides bacteria, or a combination of Bacteroides and Enterococcus bacteria as described herein. The subject can develop with minimized deficiencies or no discernable deficiencies in anxiety, repetitive behavior, and/or communication behavior. Optionally, the at-risk subject is a child, adolescent, or adult three years old or older. In some embodiments, the subject is determined to be at risk for developing anxiety. Following administration of the probiotic, the subject can develop with minimal or no anxiety. In some embodiments, the subject is determined to be at risk for developing repetitive behavior. Following administration of the probiotic, the subject can develop with minimal or no repetitive behavior. In some embodiments, the subject is determined to be at risk for developing deficient communication behavior. Following administration of the probiotic, the subject can develop with minimal or no deficiencies in communication behavior. In some embodiments, the communication behavior that develops without discernable deficiencies includes at least one of language comprehension and/or production, sociability, or communication. In some embodiments, the method further comprises determining whether the subject is at risk for schizophrenia. In some embodiments, schizophrenia symptoms are prevented.

In some embodiments, in accordance with any of the methods described above, the gut microbiotic signature of the subject is determined by analyzing nucleic acids in a sample from the subject using a suitable method known to one skilled in the art. For example, sequences of nucleic acids in the samples can be ascertained to determine the number of different species of microbes in the gut. For example, the nucleic acids from the sample can be sequenced using multiplex sequencing. For example, the nucleic acids can be analyzed on a microarray. For example, the nucleic acids can be analyzed by polymerase chain reaction (conventional or quantitative). For example, the nucleic acids can be analyzed by hybridization of a nucleic acid probe. Optionally, the nucleic acid sequences are compared to a reference, for example a nucleic acid database to ascertain the microbial species of origin. Optionally, the nucleic acids comprise the ribosomal RNA 16s subunit. Optionally, nucleic acids are isolated from the sample before their sequences are ascertained. Optionally, the nucleic acids from the sample are pooled, so that the sequences of a population of microbes can be ascertained from the pooled nucleic acids (e.g. via multiplex analysis). In some embodiments, the sample comprises a fecal sample.

In some embodiments, in accordance with any of the methods described above, the probiotic comprising, consisting essentially or, consisting of Bacteroides bacteria, or a combination of Enterococcus bacteria and Bacteroides bacteria of any of the methods described herein is selected from the group consisting of (a) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus); (b) Bacteroides bacteria (e.g., B. fragilis, B. thetaiotaomicron or B. vulgatus) and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (c) B. fragilis; (d) B. thetaiotaomicron; (e) B. vulgatus; (g) B. fragilis and B. thetaiotaomicron; (h) B. fragilis and B. vulgatus; (i) B. thetaiotaomicron and B. vulgatus; (j) B. fragilis, B. thetaiotaomicron and B. vulgatus; (k) B. fragilis and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (l) B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (m) B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (n) B. fragilis and B. thetaiotaomicron and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (o) B. fragilis and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (p) B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (q) B. fragilis, B. thetaiotaomicron and B. vulgatus and Enterococcus bacteria (e.g., E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, or E. casseliflavus); (r) B. fragilis and E. faecalis; (s) B. thetaiotaomicron and E. faecalis; (t) B. vulgatus and E. faecalis; (u) B. fragilis and B. thetaiotaomicron and E. faecalis; (v) B. fragilis and B. vulgatus and E. faecalis; (w) B. thetaiotaomicron and B. vulgatus and E. faecalis; or (x) B. fragilis, B. thetaiotaomicron, B. vulgatus and E. faecalis. Optionally, the subject is administered no other bacteria, or substantially no other bacteria apart from the identified bacteria of the probiotic, and as such the probiotic for use in treatment of the subject is in a composition or compositions free or substantially free of other bacteria. Optionally, the subject is administered no antibiotics, or is administered substantially no antibiotics, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of antibiotics. Optionally, the subject is administered no drugs, or is administered substantially no drugs, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of drugs. Optionally, the subject is administered no pharmaceutically active ingredients, or is administered substantially no pharmaceutically active ingredients, and as such the probiotic for administration to the subject is in a composition or compositions free or substantially free of pharmaceutically active ingredients.

In some embodiments, in accordance with any of the methods described above, the determination that the subject is in need of improving a behavior is made according to at least one of a behavioral assessment and/or determination of the presence, absence, and/or level of at least one biological marker from a sample of the subject. In some embodiments, for example uses, methods, and or compositions directed to infants and/or children, a subject at risk for an ASD behavior is identified based on maternal immune activation and/or other risk factors. In some embodiments, the subject is diagnosed as having ASD based on the level of an ASD-related metabolite or combination of metabolites in the gut, in a bodily fluid (for example, blood and urine), or any combination thereof. Methods of diagnosing ASD based on levels of metabolite in a subject are described in detail in US Pub. No. 2014/0065132, hereby incorporated by reference in its entirety. In some embodiments, the subject is determined to have a lesion or developmental deficiency in a region of the brain associated with speech production, speech recognition, impulse control, and/or socialization, for example regions of the cerebral cortex, the corpus callosum, Broca's area, and/or Wernicke's area. In some embodiments, an ASD behavior, for example a deficient communication, vocalization, sensorimotor, anxiety, and/or repetitive behavior, or a combination of two or more of these is identified using standard diagnostic criteria, for example in the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition (DSM-4) or Fifth Edition (DSM-5). In some embodiments, the presence or absence of ASD in the subject is determined using a behavioral test, for example at least one of the Autism Behavior Checklist (ABC), Autism diagnostic Interview-Revised (ADI-R), childhood autism Rating Scale (CARS), and/or Pre-Linguistic Autism Diagnostic Observation Schedule (PL-ADOS). The behavioral test can include, but is not limited to, detecting the presence and/or extent of 1) preoccupation with one or more stereotyped and restricted patterns of interest that is abnormal in either intensity or focus, 2) inflexible adherence to specific, nonfunctional routines or rituals, c) stereotyped and repetitive motor mannerisms (such as hand flapping, finger flapping etc.), and/or d) persistent preoccupation with parts of objects. Non-limiting examples of behavior that can be included in a behavioral test and suggest a need for improving behavioral performance in the subject under the test include: a) sensory behaviors, including poor use of visual discrimination when learning, seems not to hear, so that a hearing loss is suspected, sometimes shows no “startle response” to loud noise”, sometimes painful stimuli such as bruises, cuts, and injections evoke no reaction, often will not blink when bright light is directed toward eyes, covers ears at many sounds, squints, frowns, or covers eyes when in the presence of natural light, frequently has no visual reaction to a “new” person, stares into space for long periods of time; b) relating behaviors: frequently does not attend to social/environmental stimuli, has no social smile, does not reach out when reached for, non-responsive to other people's facial expressions/feelings, actively avoids eye contact, resists being touched or held, is flaccid when held in arms, is stiff and hard to held, does not imitate other children at play, has not developed any friendships, often frightened or very anxious, “looks through” people; c) body and object use behaviors: whirls self for long periods of time, does not use toys appropriately, insists on keeping certain objects with him/her, rocks self for long periods of time, does a lot of lunging and darting, flaps hands, walks on toes, hurts self by banging head, biting hand, twirls, spins, and bangs objects a lot, feel, smell, and/or taste objects in the environment, gets involved in complicated “rituals” such as lining things up, is very destructive; and d) language behaviors: does not follow simple commands given once, has pronoun reversal, speech is atonal, does not respond to own name when called out among two others, seldom says “yes” or “I”, does not follow simple commands involving prepositions, gets desired objects by gesturing, repeats phrases over and over, cannot point to more than five named objects, uses 0-5 spontaneous words per day to communicate wants and needs, repeats sounds or words over and over, echoes questions or statements made by others, uses at least 15 but less than 30 spontaneous phrases daily to communicate, learns a simple task but “forgets” quickly, strong reactions to changes in routine/environment, has “special abilities” in one area of development, which seems to rule out mental retardation, severe temper tantrums and/or frequent minor tantrums, hurts others by biting, hitting, and/or kicking, does not wait for needs to be met, difficulties with toileting, does not dress self without frequent help, frequently unaware of surroundings, and may be oblivious to dangerous situations, prefers to manipulate and be occupied with inanimate things, and/or a developmental delay identified at or before 30 months of age. One of ordinary skill in the art would appreciate that the attending physician would know how to identify a subject in need of treatment disclosed herein.

In some embodiments, in accordance with any of the methods described above, the method comprises administering the effective amount of probiotic in a single administration of one or more compositions. In some embodiments as described above, the method comprises administering the effective amount of the probiotic across two or more administrations of a single composition as described herein. For example, the compositions can be administered about 1 minute, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 minutes, 1 hour, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 hours, 1 day, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days apart, including ranges between any two of the listed values, for example 1 minute-10 minutes, 1 minute to 30 minutes, 1 minute to 1 hour, 1 minute-2 hours, 1 minute-4 hours, 1 minute-12 hours, 1 minute-18 hours, 1 minute-1 day, 10 minutes to 30 minutes, 10 minutes to 1 hour, 10 minutes-2 hours, 10 minutes-4 hours, 10 minute-12 hours, 10 minutes-18 hours, 10 minutes-1 day, 30 minutes to 1 hour, 30 minutes-2 hours, 30 minutes-4 hours, 30 minute-12 hours, 30 minutes-18 hours, 30 minutes-1 day, 30 minutes-2 days, 1 hour-2 hours, 1 hour-4 hours, 1 hour-12 hours, 1 hour-18 hours, 1 hour-1 day, 4 hours-12 hours, 4 hours-18 hours, 4 hours-1 day, 1 day-2 days, 1 day-3 days, 1 day-4 days, 1 day-5 days, 1 day-7 days, 1 day-10 days, 2 days-3 days, 2 days-4 days, 2 days-5 days, 2 days-7 days, 2 days-10 days, or 5 days to 10 days. In some embodiments as described above, the method comprises administering the effective amount of two or more different compositions as described herein across two or more administrations of a single composition. For example, the second composition can be administered about 1 minute, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55 minutes, 1 hour, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 hours, 1 day, 2, 3, 4, 5, 6, 7, 8, 9, or 10 days after the first composition, including ranges between any two of the listed values, for example 1 minute-10 minutes, 1 minute to 30 minutes, 1 minute to 1 hour, 1 minute-2 hours, 1 minute-4 hours, 1 minute-12 hours, 1 minute-18 hours, 1 minute-1 day, 10 minutes to 30 minutes, 10 minutes to 1 hour, 10 minutes-2 hours, 10 minutes-4 hours, 10 minute-12 hours, 10 minutes-18 hours, 10 minutes-1 day, 30 minutes to 1 hour, 30 minutes-2 hours, 30 minutes-4 hours, 30 minute-12 hours, 30 minutes-18 hours, 30 minutes-1 day, 30 minutes-2 days, 1 hour-2 hours, 1 hour-4 hours, 1 hour-12 hours, 1 hour-18 hours, 1 hour-1 day, 4 hours-12 hours, 4 hours-18 hours, 4 hours-1 day, 1 day-2 days, 1 day-3 days, 1 day-4 days, 1 day-5 days, 1 day-7 days, 1 day-10 days, 2 days-3 days, 2 days-4 days, 2 days-5 days, 2 days-7 days, 2 days-10 days, or 5 days to 10 days. In some embodiments, the probiotic is administered in a slow release formulation (for example a slow-release capsule or implant) for any of the durations described above.

In some embodiments, the probiotic is administered to the subject until an improvement in behavioral performance is observed. Optionally, the probiotic is administered to the subject after an improvement in behavioral performance is observed, for example to solidify or maintain the improved behavioral performance.

EXAMPLES

Some aspects of the embodiments discussed above are disclosed in further detail in the following examples, which are not in any way intended to limit the scope of the present disclosure.

Example 1: Adult Treatment Demonstrating Treatment of Adult MIA Mice with a Probiotic Comprising B. fragilis Corrects Deficits in Exploratory Behavior

6-week-old offspring of immune-activated mothers were given applesauce containing B. fragilis or applesauce alone for 1 week. 4 weeks after bacterial treatment, mice were tested for anxiety-like and exploratory behavior in the open field exploration assay. Adult treatment with B. fragilis significantly increased exploratory behavior in MIA offspring, as measured by increased entries into the center arena (FIG. 1A) and increased total distance traveled in the open arena (FIG. 1B). Poly(I:C) was administered as an immune activator in mothers. Offspring of non-immune activated mothers (saline treatment) were examined as additional controls. Abbreviations used in FIGS. 1A-1B: Sal=saline offspring controls, pIC=poly(I:C) offspring, NB=sodium bicarbonate vehicle, BF=B. fragilis.

Anxiety-like and exploratory behavior, as measured by entries into center area and total distance traveled in open area were significantly higher in the B. fragilis-treated adult offspring of immune-activated mothers than in untreated controls. The treated offspring would be understood to have an adult gut microbiome signature. Accordingly, treatment with a probiotic comprising, consisting essentially of, or consisting of B. fragilis can improve anxiety-like behavior and exploratory behavior in subjects having adult gut microbiomes and exhibiting ASD symptoms in accordance with some embodiments described herein.

Example 2: Adult Treatment Demonstrating Treatment of Adult MIA Mice with a Probiotic Comprising B. fragilis Reduces Repetitive Behavior in Accordance with Some Embodiments Described Herein

6-week-old offspring of immune-activated mothers were given applesauce containing B. fragilis or applesauce alone for 1 week. 4 weeks after bacterial treatment, mice were tested for repetitive behavior in a stereotyped marble burying assay. As shown in FIG. 2, Adult treatment with B. fragilis decreased stereotyped marble burying in MIA offspring as compared to untreated controls. Poly(I:C) was administered as an immune activator in mothers. Offspring of non-immune activated mothers (saline treatment) were examined as additional controls. Abbreviations used in FIG. 2: Sal=saline offspring controls, pIC=poly(I:C) offspring, NB=sodium bicarbonate vehicle, BF=B. fragilis. To test for statistical significance, a p value for a one way analysis of variance (ANOVA) with Bonferroni post hoc test was performed (shown p=0.0867).

Repetitive behavior, as measured by the marble burying test was reduced in the B. fragilis-treated adult offspring of immune-activated mothers than in untreated controls. Accordingly, treatment with a probiotic comprising, consisting essentially of, or consisting of B. fragilis can improve repetitive behavior in subjects having adult gut microbiomes and exhibiting ASD symptoms in accordance with some embodiments described herein.

Example 3: Adult Treatment Demonstrating Treatment of Adult MIA Mice (Having a Characteristic Adult Microbiome) with a Probiotic Comprising B. fragilis increases Communication Behavior in Accordance with Some Embodiments Described Herein

6-week-old offspring of immune-activated mothers were given applesauce containing B. fragilis or applesauce alone for 1 week. 4 weeks after bacterial treatment, male mice were tested for communicative behavior. as measured by production of ultrasonic vocalization in response to exposure to unfamiliar female mice. Adult treatment with B. fragilis increased number of calls produced by MIA offspring as compared to untreated controls (see FIG. 3). Poly(I:C) was administered as an immune activator in mothers. Offspring of non-immune activated mothers (saline treatment) were examined as additional controls. Abbreviations used in FIG. 3: Sal=saline offspring controls, pIC=poly(I:C) offspring, NB=sodium bicarbonate vehicle, BF=B. fragilis.

Communication behavior, as measured by production of ultrasonic vocalization was increased in the B. fragilis-treated adult offspring of immune-activated mothers than in untreated controls. Accordingly, treatment with a probiotic comprising, consisting essentially of, or consisting of B. fragilis can improve communication behavior in subjects having adult gut microbiomes and exhibiting ASD symptoms in accordance with some embodiments described herein.

Example 4: Correction of ASD-relevant Behaviors by B. fragilis

A human subject exhibits anxiety and impaired sociability. The subject is determined to have a gut microbiotic profile comprising at least 800 different microbial species via high-throughput sequencing (and alignment) of nucleic acids isolated from a fecal sample of the subject. The subject consumes a gel capsule comprising an effective amount of a probiotic consisting essentially of B. fragilis weekly for eight weeks. After about eight weeks of consuming the gel capsule, the subject is expected to exhibit improved anxiety and sociability.

Example 5: Correction of ASD-relevant Behaviors by B. fragilis

A human subject exhibits repetitive behavior and impaired language comprehension and usage. The subject is determined to have a gut microbiotic profile comprising at least 1000 different microbial species via high-throughput sequencing (and alignment) of nucleic acids isolated from a fecal sample of the subject. The subject consumes a cereal bar comprising an effective amount of a probiotic consisting essentially of B. fragilis until the symptoms are expected to improve. The subject is expected to exhibit improved repetitive behavior and impaired language comprehension and usage.

Example 5: Correction of ASD-relevant Behaviors by B. thetaiotaomicron

A human subject exhibits repetitive behavior and impaired language comprehension and usage. The subject is determined to have a gut microbiotic profile comprising at least 1000 different microbial species via high-throughput sequencing (and alignment) of nucleic acids isolated from a fecal sample of the subject, including relative quantities (from greatest to least) of the following phyla: Firmicutes>Bacteroidetes>Actinobacteria>Proteobacteria. The subject consumes a yogurt drink comprising an effective amount of a probiotic consisting essentially of B. thetaiotaomicron until the symptoms are expected to improve. The yogurt drink is substantially free of drugs and antibiotics. The subject is expected to exhibit improved repetitive behavior and impaired language comprehension and usage.

In at least some of the previously described embodiments, one or more elements used in an embodiment can interchangeably be used in another embodiment unless such a replacement is not technically feasible. It will be appreciated by those skilled in the art that various other omissions, additions and modifications may be made to the methods and structures described above without departing from the scope of the claimed subject matter. All such modifications and changes are intended to fall within the scope of the subject matter, as defined by the appended claims.

With respect to the use of substantially any plural and/or singular terms herein, those having skill in the art can translate from the plural to the singular and/or from the singular to the plural as is appropriate to the context and/or application. The various singular/plural permutations may be expressly set forth herein for sake of clarity.

It will be understood by those within the art that, in general, terms used herein, and especially in the appended claims (e.g., bodies of the appended claims) are generally intended as “open” terms (e.g., the term “including” should be interpreted as “including but not limited to,” the term “having” should be interpreted as “having at least,” the term “includes” should be interpreted as “includes but is not limited to,” etc.). It will be further understood by those within the art that if a specific number of an introduced claim recitation is intended, such an intent will be explicitly recited in the claim, and in the absence of such recitation no such intent is present. For example, as an aid to understanding, the following appended claims may contain usage of the introductory phrases “at least one” and “one or more” to introduce claim recitations. However, the use of such phrases should not be construed to imply that the introduction of a claim recitation by the indefinite articles “a” or “an” limits any particular claim containing such introduced claim recitation to embodiments containing only one such recitation, even when the same claim includes the introductory phrases “one or more” or “at least one” and indefinite articles such as “a” or “an” (e.g., “a” and/or “an” should be interpreted to mean “at least one” or “one or more”); the same holds true for the use of definite articles used to introduce claim recitations. In addition, even if a specific number of an introduced claim recitation is explicitly recited, those skilled in the art will recognize that such recitation should be interpreted to mean at least the recited number (e.g., the bare recitation of “two recitations,” without other modifiers, means at least two recitations, or two or more recitations). Furthermore, in those instances where a convention analogous to “at least one of A, B, and C, etc.” is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., “a system having at least one of A, B, and C” would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and/or A, B, and C together, etc.). In those instances where a convention analogous to “at least one of A, B, or C, etc.” is used, in general such a construction is intended in the sense one having skill in the art would understand the convention (e.g., “a system having at least one of A, B, or C” would include but not be limited to systems that have A alone, B alone, C alone, A and B together, A and C together, B and C together, and/or A, B, and C together, etc.). It will be further understood by those within the art that virtually any disjunctive word and/or phrase presenting two or more alternative terms, whether in the description, claims, or drawings, should be understood to contemplate the possibilities of including one of the terms, either of the terms, or both terms. For example, the phrase “A or B” will be understood to include the possibilities of “A” or “B” or “A and B.”

In addition, where features or aspects of the disclosure are described in terms of Markush groups, those skilled in the art will recognize that the disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group.

As will be understood by one of skill in the art, for any and all purposes, such as in terms of providing a written description, all ranges disclosed herein also encompass any and all possible sub-ranges and combinations of sub-ranges thereof. Any listed range can be easily recognized as sufficiently describing and enabling the same range being broken down into at least equal halves, thirds, quarters, fifths, tenths, etc. As a non-limiting example, each range discussed herein can be readily broken down into a lower third, middle third and upper third, etc. As will also be understood by one skilled in the art all language such as “up to,” “at least,” “greater than,” “less than,” and the like include the number recited and refer to ranges which can be subsequently broken down into sub-ranges as discussed above. Finally, as will be understood by one skilled in the art, a range includes each individual member. Thus, for example, a group having 1-3 articles refers to groups having 1, 2, or 3 articles. Similarly, a group having 1-5 articles refers to groups having 1, 2, 3, 4, or 5 articles, and so forth.

While various aspects and embodiments have been disclosed herein, other aspects and embodiments will be apparent to those of skill in the art. The various aspects and embodiments disclosed herein are for purposes of illustration and are not intended to be limiting, with the true scope and spirit being indicated by the following claims. 

1. A method for improving anxiety or autism spectrum disorder (ASD) in a subject, the method comprising: identifying a subject having a gut microbiota signature comprising at least 500 different species of microbes; and administering to the subject an effective amount of one or more Bacteroides bacteria.
 2. The method of claim 1, further comprising identifying the gut microbiota signature of the subject as an adult gut microbiotia signature.
 3. The method of claim 1, wherein the subject suffers from anxiety, autism spectrum disorder (ASD), or a pathological condition with one or more of the symptoms of ASD.
 4. The method of claim 1, wherein the effective amount of one or more Bacteroides bacteria comprises B. fragilis.
 5. The method of claim 1, wherein the effective amount of one or more Bacteroides bacteria comprises B. fragilis, B. thetaiotaomicron, B. vulgatus, or a mixture of two or three of the listed bacteria
 6. The method of claim 1, further comprising administering an amount of Enterococcus bacteria to the subject.
 7. The method of claim 1, wherein the method consists essentially of administering the effective amount of one or more Bacteroides bacteria.
 8. The method of claim 7, wherein the one or more Bacteroides bacteria is B. fragilis.
 9. The method of claim 1, wherein the effective amount of one or more Bacteroides bacteria is in a composition substantially free of bacteria other than the Bacteroides bacteria.
 10. The method of claim 1, wherein the effective amount of Bacteroides bacteria is in a composition substantially free of bacteria other than B. fragilis.
 11. The method of claim 1, wherein the effective amount of one or more Bacteroides bacteria is administered orally.
 12. The method of claim 1, wherein improving anxiety or ASD comprises improving a communication behavior, a repetitive behavior, or a combination.
 13. The method of claim 1, wherein the subject is an adult.
 14. The method of claim 1, wherein the subject is administered no antibiotics.
 15. The method of claim 1, wherein the gut microbiota signature comprises phyla, in order of greatest to least abundance, of: (a) Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria; or (b) Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria.
 16. The method of claim 1, wherein the effective amount of the one or more Bacteroides bacteria is administered in a single composition.
 17. The method of claim 1, wherein the effective amount of the one or more Bacteroides bacteria is administered in two or more compositions.
 18. The method of claim 1, wherein the gut microbiota signature comprises at least 500 different species of microbes as determined by comparison of sequences of 16s rRNA subunits.
 19. The composition of claim 1, wherein the gut microbiota signature comprises at least 1000 different species of microbes.
 20. The method of claim 6, wherein the Enterococcus bacteria is selected from the group consisting of: E. faecalis, E. faecium, E. hirae, E. avium, E. durans, E. gallinarum, and E. casseliflavus. 